java/fiji-Pombe_Analyzer_jar_1.0.0-SNAPSHOT_1/src/main/java/pombeAnalyzer/MexicanHatFilter.java
<gh_stars>0package pombeAnalyzer;

import ij.plugin.filter.*;
import ij.*;
import ij.gui.*;
import ij.process.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;

/**
 * This plugin convolves an image with a Laplacian of Gaussian (aka Mexican Hat) filter.
 *    
 * @author Dimiter Prodanov
 *
*/
public class MexicanHatFilter implements ExtendedPlugInFilter, DialogListener {

	private PlugInFilterRunner pfr=null;
	private int flags=DOES_ALL+CONVERT_TO_FLOAT+KEEP_PREVIEW+SNAPSHOT;
	private float[][] kernel=null;
	private boolean isMacro;

	private static int staticSZ = 11;
	private static boolean staticShowKernel;
	public static boolean staticSep;
	private int sz = staticSZ;
	private boolean showKernel = staticShowKernel;
	public boolean sep = staticSep;
	
	@Override
	public int setup(String arg, ImagePlus imp) {
		isMacro = Macro.getOptions()!=null;
		if (isMacro) {
			showKernel = false;
			sep = false;
		}
		return  flags;
	}

	@Override
	public void run(ImageProcessor ip) {
		int r = (sz-1)/2;
		float[] kernx= gauss1D(r);
		float[] kern_diff= diff2Gauss1D(r);
		kernel=new float[3][];
		kernel[0]=kernx;
		kernel[1]=kern_diff;
		float[] kernel2=computeKernel2D(r);
		kernel[2]=kernel2;
		if (showKernel) {
			showKernel = false;
			FloatProcessor fp2=new FloatProcessor(sz,sz,kernel2);
			new ImagePlus("Kernel",fp2).show();
		}
		if (sep)
			convolveSep(ip, kernx, kern_diff);
		else {
			Convolver con=new Convolver();
			con.convolveFloat(ip, kernel2, sz, sz);
		}
		double sigma2=(sz-1)/6.0;
		sigma2*=sigma2;
		ip.multiply(sigma2);
	}

	private void convolveSep(ImageProcessor ip, float[] kernx, float[] kern_diff) {
		FloatProcessor ip2 = null;
		FloatProcessor ipx = null;
		ip2 = (FloatProcessor)ip.duplicate();
		ip2.setRoi(ip.getRoi());
		ip2.setSnapshotPixels(ip.getSnapshotPixels());
		ipx=(FloatProcessor)ip2.duplicate();
		ipx.setRoi(ip.getRoi());
		ipx.setSnapshotPixels(ip.getSnapshotPixels());
		Convolver con=new Convolver();
		con.convolveFloat1D(ipx, kern_diff, sz, 1); // x direction
		ipx.setSnapshotPixels(null);
		con.convolveFloat1D(ipx, kernx, 1, sz); // y direction
		con.convolveFloat1D(ip2, kernx, sz, 1); // x direction
		ip2.setSnapshotPixels(null);
		con.convolveFloat1D(ip2, kern_diff, 1, sz); // y direction
		add(ip2, ipx, ip2.getRoi());
		insert(ip2, ip);
	}

	private void insert(ImageProcessor ip1, ImageProcessor ip2) {
		float[] pixels1 = (float[])ip1.getPixels();
		float[] pixels2 = (float[])ip2.getPixels();
		Rectangle r = ip1.getRoi();
		int offset = r.y*r.width;
		int n = r.width*r.height;
		for (int i=0; i<n; i++) {
			pixels2[offset] = pixels1[offset];
			offset++;
		}
 	}

	private void add(ImageProcessor ip1, ImageProcessor ip2, Rectangle r) {
		for (int y=r.y; y<r.y+r.height; y++) {
			for (int x=r.x;x<r.x+r.width; x++) {
				float sum = ip1.getf(x,y) + ip2.getf(x,y);
				ip1.setf(x, y, sum);
			}
		}
	}

	public float[] getKernel(int i) {
		return kernel[i];
	}

	@Override
	public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
		this.pfr = pfr;
		int r = (sz-1)/2;
		GenericDialog gd=new GenericDialog("Mexican Hat Filter");
		gd.addNumericField("Radius:", r, 1);
		gd.addCheckbox("Show kernel", showKernel);
		gd.addCheckbox("Separable", sep);
		gd.addPreviewCheckbox(pfr);
		gd.addDialogListener(this);
		gd.showDialog();
		if (gd.wasCanceled())
			return DONE;
		if (!isMacro) {
			staticSZ = sz;
			staticShowKernel = showKernel;
			staticSep = sep;
		}
        int flags2 = IJ.setupDialog(imp, flags);  // if stack, ask whether to process all slices
        if (!sep)
        	flags2 += PARALLELIZE_IMAGES;
        return flags2;
	}

	// Called after modifications to the dialog. Returns true if valid input.
	public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
		int r = (int)(gd.getNextNumber());
		showKernel = gd.getNextBoolean();
		sep = gd.getNextBoolean();
		sz = 2*r+1;
		if (gd.wasCanceled())
			return false;
		return r>0;
	}

	public float[] computeKernel2D(int r) {
		sz=2*r+1;
		final double sigma2=2*((double)r/3.0+1/6.0)*((double)r/3.0 +1/6.0);
		float[] kernel=new float[sz*sz];
		final double PIs=4/Math.sqrt(Math.PI*sigma2)/sigma2/sigma2;
		float sum=0;
		for (int u=-r; u<=r; u++) {
			for (int w=-r; w<=r; w++) {
				final double x2=u*u+w*w;
				final int idx=u+r + sz*(w+r);
				kernel[idx]=(float)((x2 -sigma2)*Math.exp(-x2/sigma2)*PIs);
				///System.out.print(kernel[c] +" ");		
				sum+=kernel[idx];

			}
		}
		sum=Math.abs(sum);
		if (sum<1e-5) sum=1;
		if (sum!=1) {
			for (int i=0; i<kernel.length; i++) {
				kernel[i]/=sum;
				//System.out.print(kernel[i] +" ");
			}
		}
		return kernel;
	}

	public float[] gauss1D(int r) {
		sz=2*r+1;
		//final double sigma2=2*((double)r/3.5 +1/7.0)*((double)r/3.5 +1/7.0);
		final double sigma2=((double)r/3.0+1/6)*((double)r/3.0 +1/6.0);
		float[] kernel=new float[sz];
		float sum=0;
		final double PIs=1/Math.sqrt(2*Math.PI*sigma2);
		for (int u=-r; u<=r; u++) {
			final double x2=u*u;
			final int idx=u+r ;
			kernel[idx]=(float)(Math.exp(-0.5*x2/sigma2)*PIs);

		}
		sum=Math.abs(sum);
		if (sum<1e-5) sum=1;
		if (sum!=1) {
			for (int i=0; i<kernel.length; i++) {
				kernel[i]/=sum;
				//System.out.print(kernel[i] +" ");
			}
		}
		return kernel;
	}

	public float[] diff2Gauss1D(int r) {
		sz=2*r+1;
		final double sigma2=((double)r/3.0+1/6)*((double)r/3.0 +1/6.0);
		float[] kernel=new float[sz];
		//((w^2-r^2)*%e^(-r^2/(2*w^2)))/(2^(3/2)*sqrt(%pi)*w^4*abs(w))
		float sum=0;
		final double PIs=1/Math.sqrt(2*Math.PI*sigma2);
		for (int u=-r; u<=r; u++) {
			final double x2=u*u;
			final int idx=u+r ;
			kernel[idx]=(float)((x2-sigma2)*Math.exp(-0.5*x2/sigma2)*PIs);

		}
		sum=Math.abs(sum);
		if (sum<1e-5) sum=1;
		if (sum!=1) {
			for (int i=0; i<kernel.length; i++) {
				kernel[i]/=sum;
				//System.out.print(kernel[i] +" ");
			}
		}
		return kernel;
	}

	private float[] joinXY(float[][] kernel, int a, int b) {
		int sz=kernel[0].length;
		float[] jkernel=new float[sz*sz];
		for (int i=0; i<jkernel.length; i++)
			jkernel[i]=1.0f;
		for (int m=0; m<sz; m++) { // row
			for (int n=0; n<sz; n++) { // col
				final int idx=n + m *sz;
				jkernel[idx]*=kernel[a][n];
			}
		}
		for (int m=0; m<sz; m++) { // row
			for (int n=0; n<sz; n++) { // col
				final int idx=n + m *sz;
				jkernel[idx]*=kernel[b][m];
			}
		}
		return jkernel;
	}

	@Override
	public void setNPasses (int nPasses) {
	}
        
        public void setRadious(int radious){
            sz = 2*radious+1;
        }
}
